Question: Humann2 for metatranscriptomic data
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gravatar for cook284
2.9 years ago by
cook2840
cook2840 wrote:

I have some metatranscriptomic data from a community consisting of one green alga and a mixed population of bacteria. I want to annotate the transcripts from both eukaryotic and prokaryotic community members and get pathway abundance measures so that I can compare the metabolic activities between two different treatments. The Humann2 software provides an excellent pipeline for the prokaryotic portion of my data but excludes eukaryotes. I know that you can provide custom databases to Humann2. Does anybody have an idea of a suitable eukaryotic database to format for this purpose and if this approach would work to get me a comprehensive analysis of the whole community transcript pool?

ADD COMMENTlink written 2.9 years ago by cook2840

According to the documents of HUMAnN2: MetaPhlAn2 and ChocoPhlAn pangenome database are used to facilitate fast, accurate, and organism-specific functional profiling, Organisms included are Archaea, Bacteria, Eukaryotes, and Viruses. It looks like the Eukaryotes genome has been included.

ADD REPLYlink written 6 weeks ago by Shicheng Guo8.1k
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